Each version of the game is essentially the same in storyline and format. The story begins with the Joker escaping from Arkham Asylum, and through various henchmen, trying to send Gotham City into chaos. Batman must survive several side-scrolling levels, as well as defeat five boss levels, to ensure that Gotham is safe.

Batman is armed with a utility belt that allows him to collect various types of icons throughout the stages in order to shoot different types of batarangs and projectiles. Batman only has one type of batarang in the Game Boy version. The console version of the game uses a password feature which allows players to return to any non-boss level which they have previously reached. The Game Boy version allows the player to select a level at the start of the game.

The music for the NES version was composed by Naoki Kodaka, with sound programming by Nobuyuki Hara and Shinichi Seya.[2] The Game Boy version of the game had an entirely original soundtrack composed by Manami Matsumae. For the Genesis Revenge of the Joker, Kodaka's soundtrack was adapted by Tommy Tallarico.